Types of Research

1. Fish Ecosystem Studies and Management
2. Ocean Forecasting
3. Ocean Chemistry
4. Climate and Ocean Variability, Change and Impacts
5. Marine Mammals

Affiliated Programs

1. NOAA Marine Mammal Laboratory
2. Bering Sea Climate and Ecosystem
3. Ecosystems and Fisheries-Oceanography Coordinated Investigations
4. J-SCOPE
5. Innovative Technology for Arctic Exploration
6. Cetacean Assessment and Ecology Program

Research Highlights – 2023

Archival Storage and Dissemination of Data on Northeast Pacific Fish Eggs, Larvae, and Adults

The project archives specimens collected on Alaska Fisheries Science Center surveys in the UW Fish Collection. It provides funding for graduate student, undergrad, and partial funding for collection manager Katherine Maslenikov.  Expectations are curation of the specimens, management of the data, and for the graduate student, conduct research using these specimens that are in line with the objectives for the sponsor.

Principal Investigator: Luke Tornabene
Research Theme: Marine Ecosystems

Development of innovative approaches to support sustainable aquaculture and understand the effects of ocean acidification on marine species

In this project, we include innovative problem-solving approaches to address challenges facing sustainable aquaculture development, understanding the impacts of climate variability on marine fish and shellfish, and woven throughout these research activities is the development of ‘omics and bioinformatics workflows for both data generation and data analysis (bioinformatics). Through this composite project, our goal is to contribute to applications to support sustainable aquaculture, increase our understanding of the effects of OA on marine fish and shellfish and contribute bioinformatic capacity, tools and workflows for research related to aquaculture, genomics and climate change.

Principal Investigator: Steven Roberts
Research Theme: Aquaculture Science

Mariculture research technician

The oyster industry is well poised for rapid expansion in Alaska; however, the lack of oyster hatchery capacity to produce seed in Alaska and oyster strains optimized for growth in the region presents significant hurdles for farm operations. To date, oysters have not been spawned consistently, and cost-effectively in Alaska, creating a reliance on larvae supplied from outside the state and an extreme insecurity and shortage of seed supply. The goal of this project is to resolve the scientific barriers to oyster research in Alaska by providing a research hatchery to identify cost efficiency rearing strategies to produce seed for the industry, as well as breeding oyster strains optimized for growth in Alaska. The mariculture research technician at the NOAA Alaska Fisheries Science Center will focus on the development of oyster hatchery technology in Alaska which will entail assisting in the set up and maintenance of infrastructure that supports the oysters, including maintaining the microalgae culture.

Principal Investigator: Schery Umanzor (UAF)
Research Theme: Aquaculture Science

Relationships among mercury concentrations, birth weight and future survival of Steller sea lion pups in the western and central Aleutian Islands.

Steller sea lion (Eumetopias jubatus) populations continue to decrease on rookeries in the western Aleutian Islands, Alaska where we also find significantly higher median total mercury concentrations measured in the natal hair (lanugo) of young Steller sea lions compared to pups from most rookeries to the east. In this project we test whether there is a relationship between the concentration of total mercury in the lanugo of Steller sea lion pups and the probability of survival of sea lion pups. We will also investigate whether the estimated birth weight of pups may play a role in diminished survival probability.

Principal Investigator: Lorrie Rea
Research Theme: Marine Ecosystems

Genetic Analysis of Salmon Bycatch

The National Marine Fisheries Service (NOAA) estimates the genetic stock composition of chum and Chinook salmon that are incidentally caught in groundfish fisheries conducted in the US waters of the Bering Sea and Gulf of Alaska. Recent advances in genotyping and data analysis methods have improved the ability to efficiently and accurately determine what proportion of salmon bycatch is derived from various stocks around the North Pacific and Bering Sea. The genetic stock composition estimates are being used to investigate spatial patterns in bycatch related to climatic conditions in the the Bering Sea and Gulf of Alaska.

Principal Investigator: Megan McPhee (UAF)
Research Theme: Marine Ecosystems

Using eDNA to investigate nearshore fish distributions in Alaska

This project involves using environmental DNA (eDNA) to study the biodiversity of nearshore fishes across Alaska. Specifically, research objectives include: (1) Process nearshore eDNA samples from southeast and southcentral Alaska; (2) Conduct bioinformatics of eDNA data; (3) Investigate ecological patterns using eDNA data.

Principal Investigator: Jessica Glass (UAF)
Research Theme: Marine Ecosystems

eDNA detection of climate-driven range shifts: an early warning system for the Arctic

Marine species ranges are shifting northward, driven by climate change and associated ocean warming. In the North Pacific, surveys have identified recent northward movement of walleye pollock, Pacific cod, and snow crab but the permanence and variability of these range shifts is uncertain and remains difficult to track using traditional sampling approaches. We will analyze environmental DNA (eDNA) from water samples to understand the magnitude, extent, and timing of range shifts for presence and relative abundance of high biomass fishery species.

Principal Investigator: Jessica Glass (UAF)
Research Theme: Marine Ecosystems

Non-stationary relationships between climate and fisheries in the California Current

An emerging challenge for understanding ecosystems is that relationships between species abundance and the environment are changing over space and time. Recent examples include shifting spatial distributions of fish populations, and a changing relationship between Pacific salmon and the Pacific Decadal Oscillation, a classic environmental index relating sea surface temperature to species abundance. Changing relationships have been documented in the Gulf of Alaska and Eastern Bering Sea, but are not yet fully understood in the California Current ecosystem. Using oceanographic and biological datasets, we investigate and synthesize changing relationships between physical conditions and commercial, recreational, and protected species.

Principal Investigator: Curry Cunningham (UAF)
Research Theme: Marine Ecosystems

Investigating Population Genetic Architecture in the Pacific Sardine

The purpose of this project is to leverage genomic data to improve estimates of population structure for Pacific sardines.  Specifically, research objectives include: 1) Generate whole genome sequencing data from three groups of Pacific sardines; 2) Analyze data to determine if stock structure exists; and 3) Convey results to managers and evaluate current stock assessment.

Principal Investigator: Jessica Glass (UAF)
Research Theme: Marine Ecosystems

Spatio-temporal synthesis of regional ocean model predictions and field collections for zooplankton

Climate change is impacting zooplankton, an important food source for fisheries species and marine mammals in the Eastern Bering Sea but can be difficult to study due to the ephemeral nature of the zooplankton. This project is focused on comparing the Bering Ecosystem Study Nutrient-Phytoplankton-Zooplankton (BESTNPZ) model to empirical zooplankton data to provide zooplankton biomass hindcasts that could be useful for scientists and managers who aim to predict zooplankton abundances for fisheries management. We validate the BESTNPZ model using empirical data and develop a statistical model that integrates empirical and BESTNPZ information. We use these results to suggest areas where the BESTNPZ model can be adjusted to better reflect biological processes.

Principal Investigator: Curry Cunningham (UAF)
Research Theme: Marine Ecosystems

Partnership with the Northwest Fisheries Science Center to Develop Increased Capacity in the School of Aquatic and Fishery Sciences to Enhance Teaching and Research

The purpose of this project is to create a partnership with the Northwest Fisheries Science Center to develop an increased capacity in the UW School of Aquatic and Fishery Sciences (SAFS) to enhance teaching and research in stock assessment and resource management. The broad objective will be achieved by continuing to support two tenure track faculty (Trevor Branch and Chris Anderson).

Principal Investigators: Andre Punt and Tim Essington
Research Theme: Marine Ecosystems

Forecast effects of ocean acidification on Alaska red king crab

This project will extend the bioeconomic models developed for red king crab in Bristol Bay, and eastern Bering Sea Tanner crab, to analyze the sources of uncertainty that are most influential for experimentally informed forecasts of abundance, yields, and fishery income given the effects of Ocean Acidification. It will also apply simulation-based methods to explore the trade-offs between precision of the outcomes of bioeconomic models for Bristol Bay red king crab  and the sample sizes and experimental designs for Ocean Acidification experiments.

Principal Investigator: Andre Punt
Research Theme: Marine Ecosystems

Modeling Temporal Patterns in Fish Recruitment

Simulation of future time series of fish population recruitment is an important step in fishery rebuilding analyses and other types of management strategy evaluations. This project will extend previous studies of fluctuations in fish recruitment and develop approaches that can replicate typical patterns observed in nature. This study will compare the skill of various time series methods for characterizing the variability of recruitment with the goal of guiding development of algorithms that produce realistic patterns.

Principal Investigator: Andre Punt
Research Theme: Marine Ecosystems

West Coast Groundfish Stock Assessment

The purpose of this project is to conduct research on the population dynamics and stock assessment of groundfish species occurring off the coasts of Washington, Oregon and California by developing quantitative methods for the analysis of the population dynamics of groundfish species, collaborating with National Marine Fisheries Service scientists who are conducting quantitative stock assessments of west coast groundfish species, building expertise among scientists conducting management-related research for west coast groundfish in the application of state of the art methods, and to providing support, training, and mentoring for graduate students in the field of quantitative fisheries science.

Principal Investigator: Andre Punt
Research Theme: Marine Ecosystems

Adapting monitoring to a changing seascape: increasing the efficiency, flexibility, and continuity of bottom trawl surveys in the Bering Sea and beyond

This project will evaluate the current eastern Bering Sea (EBS) shelf survey design and potential alternatives with respect to sampling efficiency, robustness to climate and species distribution variability, and flexibility to sampling constraints. It will determine whether and how the efficiency of the EBS shelf survey can be increased by using survey simulations to investigate whether alternative sampling densities or designs can achieve comparable or improved performance at lower levels of sampling effort relative to the current EBS shelf survey design, including by developing and testing static and dynamic survey designs.

Principal Investigator: Andre Punt
Research Theme: Marine Ecosystems

From climate to communities in the Gulf of Alaska: using an integrated modeling approach to evaluate drivers of present and future system-level productivity and assess climate impacts on fishing-dependent communities.

This integrated program will explore the drivers of system-level productivity under climate change, the ways that fisheries management can promote resilient fisheries in a changing climate, and development of a coupled modeling approach that extends from climate to communities to evaluate economic and social impacts of climate change on resource-dependent communities in the GOA.

Principal Investigator: Andre Punt
Research Theme: Marine Ecosystems

Population trends, vital rates, and diets of otariid pinnipeds in Alaska

This project is a partnership with the Alaska Ecosystems Program at MML to support NOAA in the assessment of Steller sea lions and northern fur seals in Alaska and along the west coast of the United States. The primary goal is to provide baseline information on Steller sea lion and northern fur seal biology and ecology. The project contributes to established, long-term studies as well as develops innovative technologies and approaches in three primary research areas: 1) population trends and abundance, 2) vital rates (survival, reproduction, and movement), and 3) diet.

Principal Investigator: Ivonne Ortiz
Research Theme: Marine Ecosystems

The Role of Cetaceans in Alaska Marine Ecosystems

The project is a partnership with the Cetacean Assessment and Ecology Program at the Marine Mammal Laboratory to inform and improve management. We support and develop data collection on the density/abundance, distribution, population genetics and stock structure, life-history parameters, timing, and behavior of cetaceans. The projects conducts: 1) surveys, 2) passive-acoustic monitoring, 3) telemetry, 4) genetics and ‘omics, 5) chemical tracers, 6) quantitative modeling and 7) research of new technologies.

Principal Investigator: Ivonne Ortiz
Research Theme: Marine Ecosystems

Abundance, trends, and distribution of Alaska seals in Arctic and sub-Arctic marine ecosystems

This project conducts multidisciplinary research to inform marine mammal management. Research includes : 1) surveys of seal abundance/distribution, based on photographic and other remote sensing methods; 2) satellite telemetry of seal movements and foraging behavior; 3) assessment of seal health, condition, diet, and stock structure based on telemetry/ tagging data; 4) development, evaluation, and application of multi-spectral digital imaging systems for use in occupied aircraft/unmanned aerial systems (UAS), and machine learning  approaches for pinniped detection and classification in the multi-spectral images; and 5) Advancing use of UAS to monitor pinnipeds in remote habitats.

Principal Investigator: Ivonne Ortiz
Research Theme: Marine Ecosystems

Marine Biological Interactions in the North Pacific – Fish Interactions

Understanding the ecological connections between marine predators and prey is central for making forecasts, advising on fisheries policies and regulations, and understanding how ecosystems work  The field portion of this project supports the Alaska Food Habits program, one of the world’s longest running continuous monitoring of feeding habits of bottom fish in Alaskan marine waters and has one of the largest databases worldwide. The food habits information, along with fish abundance, environmental, and other information  is used to develop ecosystem models, evaluate changes in the ecosystem and advance ecosystem-based fisheries management. This is particularly important to ensure the sustainability of commercial and non-commercial species given the rapid rates of environmental change that Alaskan ecosystems are experiencing. Results from this project directly inform fisheries management.

Principal Investigator: Ivonne Ortiz
Research Theme: Marine Ecosystems

Ecosystems and Fisheries-Oceanography Coordinated Investigations (Task II-FOCI)

The Ecosystems and Fisheries-Oceanography Coordinated Investigations (EcoFOCI) program is a unique collaboration bridging NOAA cross-line office programs at NOAA Research’s Pacific Marine Environmental Lab and NOAA Fisheries Alaska Fisheries Science Center. EcoFOCI is a ~35-year umbrella program between Fisheries Oceanography Coordinated Investigations (FOCI/PMEL) and North Pacific Climate Regimes and Ecosystem Productivity (NPCREP/AFSC). Our mission is to understand the dynamic relationships among climate, fisheries, and the marine environment to ensure sustainability of Alaskan living marine resources and healthy ecosystems. EcoFOCI scientists accomplish these goals through an integration of field, laboratory, and modeling studies, from physics to fish, to determine how varying biological and physical factors, including climate, influence Alaska’s Large Marine Ecosystems and specifically commercially valuable fish species. The intent of this research is to improve scientific understanding, provide guidance for resource managers on climate adaptation and resource management strategies.

Principal Investigator: Calvin Mordy
Research Theme: Marine Ecosystems

Satellite analysis of shifts in phytoplankton community composition and energy flow in the new Arctic

In situ observations of phytoplankton communities in the arctic are limited in their temporal and spatial coverage. This project is utilizing ocean color data from Visible Infrared Imaging Radiometer Suite (VIIRS) and Moderate Resolution Imaging Spectroradiometer (MODIS) and ground truth from in-situ data to address these limitations. The framework developed in this study will be applicable for the next generation of satellite products, filling a crucial knowledge gap and allowing better application of satellite data to Arctic ecosystem studies.

Principal Investigators: Calvin Mordy and Jens Nielsen
Research Theme: Marine Ecosystems

Accounting for trophic relationships in EFH designation: Essential Fish Habitat project status report

The objectives of this project are to characterize the relationship between forage fish density and remotely-sensed (satellite) chlorophyll a (chl-a) on the Bering Sea shelf. Using long-term survey data,we assess a) how changing environmental conditions, such as temperature, phytoplankton, and zooplankton abundances correspond to changing forage fish (e.g., capelin, herring and age-0 pollock) densities, b) if there is spatial overlap between chl-a hotspots and fish density hotspots, and c) how these relationships vary with climate shifts? The proposed project directly addresses Core Essential Fish Habitat (EFH) Research Priority 1: to characterize habitat utilization and productivity, increase the level of information available to describe and identify EFH; and Research Priority 2: apply information from EFH

Principal Investigators: Calvin Mordy and Jens Nielsen
Research Theme: Marine Ecosystems

Transitioning an inversion model that integrates acoustic data for euphausiid biomass estimation to open-source software

The central objective of this project is to provide a well-documented addition to the new open-source Python EchoPro package that contains the core computational functionality of the current Matlab krill biomass program and provides basic visualization capability of the analysis results. The new software package will contain an Application Programming Interface (API) that can be invoked in a reproducible manner and accept configuration of key analysis parameters and other run-time setups via a machine and human-readable configuration file. Compared to the current Matlab program, it will provide a more flexible and accessible capability to support an ecosystem-based management approach that include krill, hake and other marine organisms.

Principal Investigators: Wu-Jung Lee
Research Theme: Environmental Data Science

Environmental DNA in Support of Fisheries Assessments and Biodiversity Monitoring

Living things shed DNA into the environment, where it can be collected and sequenced, essentially mapping the species present at a given time and place. This project develops a quantitative evaluation of eDNA collected from nearly 1,000 sampling locations during a cruise spanning most of the US west coast (1,000s of km) – to our knowledge, one of the most comprehensive eDNA sampling efforts anywhere – in the context of NOAA Fisheries’ core competency in stock assessment and management. In addition, we are further analyzing eDNA collections from nearshore estuarine habitats around Puget Sound. Our research provides an opportunity to understand the appropriate spatial scale for eDNA sampling, and the potential value and pitfalls of eDNA surveys for understanding patterns of fish abundance at ecological and fisheries-relevant scales.

Principal Investigator: Ryan Kelly
Research Theme: Marine Ecosystems

Deep Learning Applications for Fish Ageing – Task III-Deep Learning

Fish ages, which are critical for managing stocks, are used to estimate growth rates, mortality, age at maturity, and population trends. Unfortunately, traditional age estimation methods of fish otoliths are labor-intensive and subject to poor repeatability. Therefore, we propose to develop an artificial intelligence System that can process FT-NIR spectra and RGB images of fish otolith. This work will target two economically valuable species: walleye pollock (Gadus chalcogrammus) from Alaska and red snapper (Lutjanus campechanus) from the U.S. Gulf of Mexico (GOM). We will evaluate the performance of our AI system and compare its performance to traditional ageing and existing human‐developed chemometrics models of spectral data.

Principal Investigators: Aotian Zheng
Research Theme: Environmental Data Science

Task II-AOOS

This project is a component of the PMEL Sustained Seasonal Forecasts of Ocean Acidification Variability in Washington and Oregon Waters, using a seasonal ocean prediction system which includes carbonate variables (J-SCOPE, JISAO’s Seasonal Coastal Ocean Prediction of the Ecosystem). J-SCOPE has been designed to provide quantitative forecasts of ocean properties under the auspices of the California Current Integrated Ecosystem Assessment (IEA). This ongoing project expands on work performed under previous support from the NOAA Ocean Acidification program, and complements other projects supported by that program.

Principal Investigator: Albert Hermann
Research Theme: Marine Ecosystems

Validation of regional ocean model hindcasts for zooplankton biomass via comparisons with thirty years of field sampling data in a rapidly changing ecosystem

Climate and ecosystem scientists use models to forecast future ecological systems under a warming planet.  In the Bering Sea Ecosystem, these models have been extensively developed, but their ability to predict the floating plankton components of ecosystem has not been explored.  Here we use an extensive data set of the zooplankton – organisms that consume algae and are important prey for a number of commercially valuable fish species – by comparing field observations with model predictions.  We will be examining the context – the time, area, and species types, where predictions are robust and where they are not.

Principal Investigator: Timothy Essington
Research Theme: Marine Ecosystems

Seasonal Forecasts of Ocean Acidification for the Bering Sea, Task II-CESM Aragonite

This project uses a combination of regional model output and in-situ data from ships and autonomous vehicles to improve our scientific understanding of ocean carbon cycling and acidification in the Bering Sea.  Model output has generated both long-term projections for changing ocean chemistry in the Bering Sea for use in strategic fisheries management planning, along with short-term term forecasts and historical hindcasts used for tactical planning and producing products for the fisheries management pipeline.  These products support NOAA Fisheries through the Ecosystem Status Report and Ecosystem and Socioeconomic Profiles.

Principal Investigator: Darren Pilcher and Wei Cheng
Research Theme: Marine Ecosystems

Task II-Genomics

The CICOES ‘Omics program leverages the advances in molecular biology to modernize ecosystem assessments and scale biological measurements with physical and chemical processes across oceanographic cruises and moored buoys. Co-located biological and ocean condition measurements allow for characterization of marine ecosystem responses to climate change manifested through warming, ocean acidification, and hypoxia. Our efforts span scales from understanding species specific impacts through indicators of stress, acclimation, and adaptation, to characterizing community wide impacts through measurements of composition, structure, distribution, and abundance. These results provide a holistic understanding of marine ecosystem responses to changing ocean conditions.

Principal Investigator: David Butterfield
Research Theme: Marine Ecosystems

Updating J-SCOPE forecasts of ocean conditions to support modeling efforts of Pacific hake habitat distribution

The overarching goal of this project is to develop a biomass-based seasonal forecast model of Pacific hake distribution as a function of oceanographic conditions. Pacific hake is the most abundant groundfish species in the California Current Ecosystem and comprises the largest groundfish landings by volume in the commercial groundfish fishery. The hake population is exploited by both U.S. and Canadian fleets and it’s jointly monitored by a U.S.-Canada acoustic survey that provides the index of abundance that is the basis for the stock assessment and management advice.

Principal Investigator: Nicholas Bond
Research Theme: Marine Ecosystems

Acoustic tracking of transboundary fish species in the Bering Sea and comparison of broadband and narrowband acoustic measurements

The primary focus of this work is to use upward looking echosounders to quantify the transboundary (US-Russia) seasonal movements of walleye pollock in the Bering Sea. These data will be used to establish seasonal estimates of walleye pollock abundance and movement through the areas. In addition, quantitative comparisons between echo-integrated data from two echosounder operating in two modes (broadband versus narrowband transmit pulses) will be made. If the comparisons yield comparable results, this will permit a fisheries related surveys to leverage the additional data inherent in the use of broadband pulses, which has not yet been demonstrated.

Principal Investigator: Christopher Bassett
Research Theme: Marine Ecosystems